File:Robust-Time-Estimation-Reconciles-Views-of-the-Antiquity-of-Placental-Mammals-pone.0000384.g004.jpg

English: In this worked example using a symmetric 32-taxon tree (Figure A), a global molecular clock holds, except for a short-term increase in evolutionary rate along one branch (the red line in Figure A). The true root time was set to 80 mya, and the times at the internal nodes are 48, 56, 64, and 72 mya. The deep internal branch (the red line in Figure A) is given an evolutionary rate ten times that of the remaining edges. The various cost functions were minimized subject to two calibrated nodes (the red numbers 1 and 2 in Figure A), using the exact branch lengths of this example as input data. The cost functions FIR, FLOG, and FADD inferred the weighted trees of Figures B, C and D, respectively. Figures E–G show the trace of evolutionary rates along the lineages from the root to taxa numbers 5, 9, and 25 of Figure A, respectively. The inferred age of the root for each cost function is shown with an arrow. The function FIR recovered the original pattern of rate change, whereas the other two functions inferred far more gradual changes, which resulted in a substantial overestimation of the root time.